Fig. 6

Comparisons of parasite detections using qPCR and shotgun sequencing. a Comparison of average Ct (cycle threshold) values are shown along the y-axis for ANTS (to the left of a), Cryptosporidium spp., Entamoeba histolytica, and Giardia lamblia. The x-axis corresponds to log10-transformed total k-mers from shotgun metagenomic sequencing. A lower average Ct translates to an earlier cycle fluorescence threshold and higher initial parasite genomic copy number. Lower Ct values have higher total k-mer counts and correspond to a higher copy of parasite genomes. The dashed line represents the Ct value of the highest standard. Blue dots along the y-axis represent positive controls, which were not shotgun sequenced. Filled dots are samples that were positive in qPCR detection, and green filled dots were simultaneously positive in fecal microscopy. b Metagenomic read counts in samples that were qPCR tested for Entamoeba histolytica only; however, given the amount of hits to qPCR negative targets, we only looked at reads assigned to species of Entamoeba known to infect humans